Prick Of A Thorn
by Tamilda
Summary: Jack and The Doctor return to Cardiff and see the changes, needing to take a trip to the future to see how things turn out. With a time limit to save the world, they need the help of one surprising young girl to save them all. Full Description inside.


**Description: Jack and The Doctor have managed to find each other again. Jack felt pulled to return to Cardiff, 2009 while The Doctor sensed that they need answers from Cardiff, 2027. With the Earth under threat yet again, it's up to Jack, The Doctor, and their surprising tag-along to save it before The Doctor will once again go flying into the stars while leaving everyone to decide what they want. **

**This story will have 2 or more main "Parts" the 2nd part will have it's own description. At the beginning of this story the focus will seem to be more on Torchwood but as we continue the focus will shift to Doctor Who.  
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**Author's Note: Besides the description, this story is going to have a few different plot lines, it's going to be long. This story takes place after Torchwood season 3 and Doctor Who Season 4. Kind of Gwen/Jack. Sorry. Be prepared for surprises!**

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**_Prick Of A Thorn_**

**_Part 1_**

******Chapter One**_  
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As Captain Jack Harkness ran through the hallways of the airship, red lights flashing and alarms blaring, he never expected who he was about to run into. The ship had been on near collision with one of the nearby planets, the engines failed and the ship drifted away at top speeds. Somehow, they had navigated away from the planet, which was full of life, but were now in danger of freezing, the heat shields had failed and if they didn't get them back on line, everyone on the ship would die. Jack did the only thing he could think of and was on his way to the control room to see if the needed repairs were out of his area of expertise. He had just turned the corner and slammed into someone, sending both of them flying backward. Jack sat up in confusion, looking at the other person who was sitting on the ground, holding his head. The man across from him was skinny with a brown suit and red converse. His brown eyes were bewildered behind his square-shaped black glasses and his hand was on his head, touching his lush brown hair. Jack stared for a few seconds, not willing to believe his eyes.

"Doctor?" He asked. The man snapped his head up.

"Jack? Jack!" He hopped to his feet with surprising agility and lifted the Captain up from the ground and patting his shoulder, "Great to see you again. Unfortunately, I need to get to the controls before we all freeze to death." The last of the time lords looked around, making Jack smile.

"I was headed there myself, and you're going the wrong way." He said. Without waiting for a response he took off, running back up the hallways with The Doctor in pursuit. "Never thought I'd see you again." He said conversationally as the two men ran.

"It seems inevitable." The Doctor responded offhandedly, "But you, Jack, you're an awful long way from where I dropped you off."

"I was craving an adventure. Here it is." Jack stopped outside a large metal door. The Doctor moved in front of him, pointing his blue-tipped sonic screw driver at the key pad. After a few minutes, the light above it turned green and the door slid open. The Doctor then moved inside, locating buttons and wires, doing things that Jack couldn't follow in order to save the ship. "I assume you're the reason we suddenly changed course." Jack commented as the Time Lord worked.

"Of course. That's Arbetrair, filled to the brim with Beters, lovely people." He answered distractedly, not looking up from his work, "So what are you doing way out here? I thought you were supposed to be in Cardiff, on Earth."

"I told you, adventure." Jack answered. The Doctor stripped a couple of wires and fused them together, shaking his head.

"No. If you wanted adventure you would have come with me when I asked. You insisted that all you wanted was to work with your little group, protecting the rift, and run Torchwood." With one last click of a button the engines around them started up again, the alarms stopped and the red lights no longer flashed. The Doctor programmed the autopilot and the airship turned itself around. Finished, he turned to look at Jack sternly, "What happened?" He asked seriously.

"Nothing." The Captain insisted.

"Jack," The Doctor titled his head, "Don't lie to me. What happened to your team?"

"They died." Jack answered, frustrated, "Happy?" The Doctor didn't day anything, and he didn't move, he continued to watch his old friend with an arched eyebrow, "They're dead, and it's all my fault. It's all because of Torchwood that they put themselves in danger, and it killed them."

"I'm so sorry." The Doctor said solemnly, he pushed himself away from the control panel and headed for the door, "Come on, I'm parked upstairs, I'll give you a ride." The two started walking without urgency back into the heart of the airship, "Are they all gone?"

"All but me, and one other."

"Who?"

"Gwen Cooper."

"Gwen Cooper!" The Doctor repeated with a big smile, "Oh, I like Gwen Cooper. Brave in the face of death, she was. How is she?"

"I don't know." Jack answered ruefully, "I haven't seen her in a while." He sucked in a sharp breath, "She told me that I couldn't run away, and I didn't want her to be the last one of us standing, but I had to get away."

"And how did that go?" The Doctor asked.

"Not so great. Hitch-hiking across the galaxy is hard, and I preferred chasing aliens down."

"You miss Torchwood." The Doctor surmised. Jack merely shrugged. The two of them reached another metal door that The Doctor once again opened, inside was a blue Police Box that brought a smile to Jack's face. The Tardis brought back many adventurous memories that he sorely missed. The Doctor leaned against it's blue side and crossed his arms, looking at Jack. "Where to?" He hesitated, not entirely sure where he wanted to go. He felt defeated, he felt like he couldn't handle exploring new worlds, he wanted a small one. "If it makes any difference," The Doctor said as he opened the Tardis door, "I'd much rather see Torchwood in the hands of someone I trust." Jack did miss it, he missed everything about it. He missed the Hub and the aliens, he missed rift activity and Gwen Cooper.

"To Cardiff, then." Jack followed The Doctor into the Tardis, "As close to 2009 as possible, that's when I left."

"Cardiff, 2009. Got it." The Doctor threw a lever and with the heavy metallic sounds that only the Tardis could make, they took off. "I'm not sure how close I got." The Doctor commented a few minutes later, solid ground once again below the big blue box. He went to the door and peeked out, when he brought his head back in, one of his eyebrows was once again arched, "Allow me to express my surprise." He said. Jack walked down the plankway and stepped into the sunlight. They were in Cardiff, all right. Jack stood facing the Wales Millennium Centre. He turned slightly to the right to see only part of the monument where Torchwood used to be.

"There was an incident." Jack explained with a small smile, "Long story short: it exploded. But they're rebuilding it so it can't be too far off." The Doctor stepped out of the Tardis and turned to lock the door behind him.

"Where to?" He asked, turning away from the blue doors and slipping the key into one of the pockets of his brown trench coat. Jack glanced back at him, he wasn't sure where he should go. The only place that would occur to him would be Torchwood, which was destroyed and being built upon. Gwen and Rhys had been planning on moving into a house and, at the moment, he had no way of finding them. Before he could open his mouth to answer, the hairs on the back of Jack's neck stood up, the feeling that he was being took over and he wheeled around, eyes scanning the area. The person watching him made no attempt to hide it. She sat at one of the tables, glaring at him out of hazel eyes that were shaded by black bangs. The rest of her hair rested just below her shoulders, her arms crossed as she regarded the two men and the blue box. Jack froze, eyes wide and guilty. The Doctor stepped up next to Jack and followed his gaze, searching for the distress. When his eyes rested on the table his face broke into a big grin. Without hesitation, he walked right up to the table, leaving Jack little choice but to follow.

"Gwen Cooper!" The Doctor beamed when he reached the table, holding out his hand.

"Doctor. Good to see you again." Gwen stood and accepted The Doctor's hand with a small smile. Then her eyes moved to Jack and the smile faded immediately.

"Gwen." Jack nodded stiffly.

"Jack." She replied coldly, "What a surprise."

"You're mad." Jack observed, wincing, "That's understandable, but I'm back now."

"For _how long_, Jack!" Gwen shook her head hopelessly, "Twice you've run off, how long will it take you this time?"

"Hear me out," He held out of his hand, "I'm here now, and I've run away enough. I don't plan on leaving any time soon." Gwen didn't look convinced, but she pushed some of the coldness out of her eyes. Jack glanced first at the rebuilding tower, then at Gwen's lack of a bulging stomach, "How long was I gone for?" He asked.

"Time machines aren't as accurate as you'd believe." The Doctor explained quickly with a rueful smile.

"It's 2010. You've been gone a year, Jack." Gwen answered.

"What are you doing out here by the bay?" Jack asked. Gwen stiffened.

"I'm meeting someone."

No sooner had the explanation left her lips than a voice from nearby called, "Gwen!" All three of them turned to see a middle-aged woman walking towards them, holding a small child in her arms. She walked up to the group and deposited the child into Gwen's arms, "She was a perfect little dear."

"Thank you, Mrs. Athers." Gwen said awkwardly, "I'll see you tomorrow." With a nod, Mrs. Athers walked back into the crowd, leaving Jack and The Doctor looking stunned and Gwen looking uncomfortable, "Sitter." She explained.

"I see you had your baby." Jack said breathlessly. The Doctor cocked an eyebrow and looked at Jack accusingly.

"Really, Jack?" He asked. Jack stared at him for a moment before leaning back.

"What? No! I know what you're thinking and no." He waved his hands in front of him vigorously. The girl in Gwen's arms squealed, bouncing herself up and down. Her hair was white-blond and cut straight around her ears. Her skin was pale and her body and limbs were small. Her eyes were big, round, and Hazel like her mother's. The squealing continued.

"Hush, Rose." Gwen bounced the girl in her arms, "Behave now, there's a good girl." She looked up to see both Jack and The Doctor frozen in place, eyes wide and trained on her small daughter.

"Rose?" Jack choked out finally, "How'd you come up with that name?"

"I don't know." Gwen shrugged, looking at each of their faces with equal confusion, "Why, what's wrong?"

"Nothing." Jack cleared his throat and focused his eyes back on Gwen.

"Rose isn't her full name, mind you. This is Toshiko Rose Cooper, Rose is what she responds most to and it's a lot easier. She's ten months old." She looked adoringly at the girl in her arms, Toshiko Rose Cooper grinned back, showing her tiny teeth. Gwen looked back at Jack with concern, "Do you not like the name?"

"It's perfect." Jack assured her. Carefully, he took a step forward a laid a comforting hand on her shoulder, "I was surprised at first. But I love it." The corners of Gwen's mouth tipped up into another small smile.

"That means a lot." She said softly. The Doctor was looking at the tower that was being rebuilt.

"What happened here, exactly?" He asked.

"There was a bomb planted in Torchwood headquarters." Jack explained, not mentioning that the bomb was actually implanted inside of _him_, "When it exploded it took the tower with it."

"Ah." The Doctor continued to look at the tower with interest.

"So, Gwen, what are you doing now?" Jack asked conversationally. Gwen smiled and raised her eyebrows.

"What else do I know how to do? I'm Torchwood." Her grin widened as both Jack and The Doctor's heads snapped to her.

"What?" Jack stuttered, "But-"

"It's a little hard to explain. Want to see it?" Gwen turned her body to face the bay, twisting her neck to look at the men. They followed her across the plaza and down to the bayside, entering the same small office that had been used as Torchwood's cover before Jack left. Gwen entered a code into a keypad situated next to the old tunnel door. After the code had been entered, she shifted Rose on her hip as a small panel flipped out. Without hesitation, Gwen pressed her thumb against the small panel, it blinked green and the metal door slid open. She turned to the time-travelers as they all walked through the door. "Thankfully for us, this part and most of the tunnel weren't destroyed in the blast. And the cell area was left surprisingly intact, a bit of a mess, though." Another metal-cog door slid open, revealing a big open cavity. The walls and floor were cement and there was a metal platform raised in the center. High-tech equipment was on tables and set around by the walls. Computers sat on impersonal desks with metal stools in front of them. Across the room were stairs, one led up to a room with windows that looked like an office, there were also a couple other rooms up there. There was also an opening that lead to the medical examining area, and next to that were stairs going down to a lower level. "Excuse the mess and lack of decor, we're in the process of rebuilding, you see."

"Do you think it was a good idea to rebuild on our old location?" Jack asked sternly, seeing many flaws in her initiated plan to pick up the pieces of Torchwood.

"All in good time." Gwen assured him as she stepped forward to the platform, "Sweetie." She said to Rose. The little girl in her arms lifted her small hands and pressed them over her ears. Gwen looked up and shouted, "I'm back! Everyone get out here, we've got company!"

"Oh, there's more." The Doctor smiled, looking around at the facility. Jack, however, was frowning.

"Gwen, I don't think you've thought this through." He insisted.

"I have." Gwen snapped, "If you'll just listen for a few minutes." A young woman with brown skin and dark brown, chin-length braids came around the corner of the stairs across the room with her gun drawn. She sidled, up to Gwen, her brown eyes alert.

"Everything okay?" She asked suspiciously, looking back and forth between Jack and The Doctor.

"Great. Guns." The Doctor crossed his arms unenthusiastically, Jack elbowed him in the side.

"Everything's fine, put the gun down." Gwen told her companion, "Where are the others?"

"They're on their way." The woman answered. Less than a minute later they were joined by two men. The first had long black dreadlocks and dark eyes, his face was broad and filled with humor, his body was bulging with muscle and tone, his skin was a slightly richer brown than the first woman who came out. The second man had intelligent blue eyes and shaved blond hair, he was wearing a white lab coat and elastic gloves.

"Where's Lina?" Gwen asked, looking up and down the line.

"She'll be here in a minute, she got a bit distracted." The man with the dreadlocks said with a smile. Gwen nodded.

"Right then, I suppose we can start the introductions without her. Everyone, this is Captain Jack Harkness, he used to be in charge of this unit. And this is The Doctor, the world-saving Time Lord we've all heard so much about. Jack, you'll remember Lois Habiba." Gwen rested her free hand on the woman's shoulder. Lois smiled and nodded humbly.

"Very good to see you again." She said, Jack inclined his head in acceptance.

"This is our Medical Expert, Nathan Worski." Gwen indicated the man in the lab coat, he waved a gloved hand. "And this," Gwen walked down the line and proudly propped her hand on the last man's shoulder, "Is our brawn, Remington Isaac. He actually is a survivor of Torchwood One."

"It's not a lifestyle you leave behind very easily." Remington explained, "Gwen was lucky enough to have come across me while screening for new members here." He smiled at Gwen, who grinned back.

"Now." Gwen handed Rose off to Lois and everyone sat down at various desks, Jack and The Doctor pulled up a couple of chairs, "I think it's time for an explanation. I have a bit of an attachment to Torchwood and what we do. You might have been able to leave and see only the bad, but I didn't. I knew that the world needed Torchwood, you felt like that once, Jack. I first went to Lois, since she was so helpful during the 456 crisis, and we started rebuilding. All of our software and files were stored on an off-base server so our old information was easily recovered. Then there was the question of equipment. We're still attaining a lot of basics, some equipment holding blocks protected the items from the blast, so we had that going for us, and we also had the holding cells, as I already said. I used the Torchwood server to screen for anyone else that might be helpful, that was how we found Remington. He'd been working for Torchwood One and managed to make it out alive, he'd been free-lancing ever since. When we contacted him he agreed to join up and with him he brought a lot of standard Torchwood equipment. He'd been high-ranks so he already knew a lot about what we use."

"Gwen," Jack interrupted, "The entire government knew about the explosion, they know that this is Torchwood and you're rebuilding it in the same spot."

"I told you not to worry about that." Gwen waved her hand dismissively, "That's the next part of the story. We needed a technician and someone with hard skin. So we got a government agent, now an ex-government agent, but she helped us wipe memories and cover up the reasons for the Torchwood explosion. Then she came to work with us."

"Who's the technician?" The Doctor asked.

Gwen opened her mouth to answer, but before she had the chance to speak a voice cut her off from the stairs, "Me." Everyone turned to see an older, Asian-appearing woman. Her black hair was tied back in a low ponytail and her cold, dark eyes surveyed the room habitually as she walked forward to the gathering. Jack felt himself stiffen at the sight of the familiar woman.

"Oh, there you are." Gwen smiled and, much to Jack's surprise, hugged the woman around her shoulders before introducing her, "Jack, you'll remember Angelina Johnson." Jack remembered her very well from his last few days at Torchwood, and he wasn't sure how he felt about seeing her now. Angelina Johnson, or Lina, looked at him nervously.

"I know that you're probably still upset with me." She said at once, "I would be, too. But I'm different. I was brought up to protect the state, and the best way to do that is here."

"Gwen, are you sure about this?" Jack asked with his jaw clenched. His friend tipped her head up stubbornly.

"Of course, I'm sure. Lina is one of our most valuable assets."

"But she's with the government!" Jack argued, "She shot me, more than once, I might add. She planted the bomb that blew up the Hub and then hunted us like dogs. She buried me in cement and took my family hostage."

"I was under orders." Lina straightened her back, unintimidated.

"And you'll remember that it was with _her_ help that we were able to save millions of children." Gwen stated firmly, "I trust her and she's proved herself time and time again. It's because of her that we've been able to rebuild here and regain some of our technology." The Captain crossed his arms, he trusted Gwen's judgment and, in the end, Lina _had_ been the key to saving the children, no matter what the personal price for either of them. "Nathan is our latest asset. He was a brilliant surgeon but his ethics had him blacklisted, we needed a doctor. We keep him under tight surveillance." She ruffled Nathan's hair playfully, "But we haven't had any trouble with him yet."

"I'm impressed." The Doctor admitted, "The 21st century taking control of the future. Very human."

"We'll take that as a compliment." Remington laughed. His laugh was cut short by the sudden blare of an alarm. Lina shot to her computer and started punching keys.

"Rift activity." She said, eyes glued to the screen, "Doesn't seem very big though, but it's possible something still got through. We should send someone to check it out."

"Right." Gwen nodded, "Lois, Remington, check it out. Keep your coms on and report as soon as you get there. Lina will give you directions, keep guns holstered for now, there's no threat detected at the moment."

"Got it." Lois said, she stood hand tucked Rose back into her mother's arms. Then she followed Remington out the cog door.

"Lina, have you got a fix?" Gwen looked over Lina's shoulder to the computer, "Nathan, get back to work." Nathan nodded and headed back down to the medical area.

"I've got a fix." Lina pressed her com, "Lois, Remington, head west." Gwen moved away from the computer and looked around, seeming a little confused. She walked up to Jack and The Doctor before stopping. Jack stood automatically.

"Jack, could you take Rose for a moment?" She leaned away from her daughter's body to let Jack take her. Jack, however, hesitated.

"I don't know..." He muttered.

"Come on, Jack. We've all got to take turns holding her, it's what we do. I need to look something up and I can't when I'm holding on to her." Gwen held Rose out more persistently. Jack carefully put his hand under the little girl's arms and lifted her. As soon as she was clear, Gwen turned and ran to her computer, typing keys frantically. Jack held Rose out in front of him for a moment, looking at her. She looked back, her head cocked and her marvelous hazel eyes wide. He placed the baby on his hip and stepped back to stand next to The Doctor.

"Are you okay?" The Doctor asked, seeing the way he looked at Rose, his eyes filled with confusion and pain.

"I'm fine." Jack answered, "I'm trying to decide if I want to stay."

"Why would you want to leave?" The Doctor asked in surprise, "You love Torchwood. And look at your brave soldiers here, they need you."

"They get along fine without me."

"They'd get along better _with_ you."

"Toshiko Rose Cooper." Jack whispered, looking at the docile child in his arms, "Gwen Cooper's daughter. It's kind of hard to believe. What a name."

"Astounding."

"Gwen is really important to me, but I think this changes things." Jack admitted.

"I don't think Gwen would want to raise the child without you. Torchwood needs you." The Doctor looked at the little girl just as Gwen walked over.

"Thanks." Gwen took her daughter back from Jack and shot him a smile, "It's good to have you back." Jack nodded and Gwen walked away.

"I just wish I knew." Jack told The Doctor under his breath, "I wish I knew what she'd grow up to be. I wish I knew how this place would turn out in a few years."

"The future can change." The Time-Lord warned, "Past can be rewritten, it can be dangerous." He looked down and sighed, "But, I think we can take a trip. See Toshiko Rose a bit more grown up."

"I thought you couldn't travel along someone's personal timeline." The 51st-Century man looked at him in confusion.

"I'd be lying if I said I haven't done it before." The Doctor rubbed the back of his neck, "And I've got a feeling about this one. Come on, let's go. We'll be back tomorrow." It took Jack a minute to catch up with The Doctor's abrupt suggestion.

"Gwen!" He called across Torchwood, Gwen looked up, "I'll see you tomorrow." He said. Gwen smiled and nodded before turning to work. "It's good to be back." Jack smiled as he followed The Doctor back out to the Tardis. They entered the blue box and, with a great deal of noise, it disappeared.

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**I'm very excited for this story even though this chapter is lamely written (not to mention the description). PLEASE stay tuned because this was the slow chapter and it will get better. **

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